2025 Landing Page Updates

.github/workflows/preview.yml

@@ -0,0 +1,21 @@
+name: Curvenote Deploy Preview
+on:
+  pull_request:
+    branches: ['main']
+permissions:
+  contents: read
+  pull-requests: write
+concurrency:
+  group: 'preview-pages'
+  cancel-in-progress: false
+jobs:
+  build-and-deploy-preview:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy Preview 🚀
+        uses: curvenote/action-myst-publish@v1
+        env:
+          CURVENOTE_TOKEN: ${{ secrets.CURVENOTE_TOKEN }}
+        with:
+          preview: true
+          preview_subdomain: microscopy-myst_preview

editors.md

@@ -1,31 +1,54 @@
 ---
 title: Editors and Developers
-description: Elemental Microscopy is headed up by Editor-in-Chief, Colin Ophus and is part of the Microscopy Society of America.
+description: Elemental Microscopy is headed by Editor-in-Chief, Colin Ophus, Technology Editor, Georgios Varnavides, and is part of the Microscopy Society of America.
 ---
 
-## Editor-in-Chief
+## Editors
 
-`Colin Ophus` is a staff scientist at NCEM, part of the [Molecular Foundry](https://foundry.lbl.gov/), at [Lawrence Berkeley Lab](https://www.lbl.gov/). He runs both a research group and user program focused on methods, algorithms, and codes for simulation, analysis and instrument design for STEM and TEM. He has received a US DOE Early Career award (2018) and was awarded the [Burton Medal](https://www.microscopy.org/awards/bios/burton_physical_2022.cfm) from the Microscopy Society of America (2022). He is project leader for the [Prismatic](https://prism-em.com/) STEM simulation and [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source codes. (cophus@gmail.com)
+`Colin Ophus` is an Associate Professor in the [Department of Materials Science and Engineering](https://mse.stanford.edu/) at [Stanford University](https://www.stanford.edu/), and a Center Fellow at the [Precourt Institute for Energy](https://energy.stanford.edu/). 
+He was formerly a staff scientist at the [National Center for Electron Microscopy](https://foundry.lbl.gov/about/facilities/the-national-center-for-electron-microscopy-ncem/), part of the [Molecular Foundry](https://foundry.lbl.gov/), at [Lawrence Berkeley National Lab](https://www.lbl.gov/). 
+He researches experimental methods, reconstruction algorithms, and data analysis for S/TEM. 
+He has received a US DOE Early Career award (2018) and was awarded the [Burton Medal](https://www.microscopy.org/awards/bios/burton_physical_2022.cfm) from the Microscopy Society of America (2022). 
+He is project leader for the [Prismatic](https://prism-em.com/) STEM simulation and [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source codes. 
+He is the founding editor-in-chief for `Elemental Microscopy`. 
+[Email](mailto:cophus@stanford.edu)
+[Website](https://colab.stanford.edu/people)
+
+
+
+`Georgios Varnavides` is a [Miller Fellow](https://miller.berkeley.edu/) postdoctoral researcher working at the University of California, Berkeley and Lawrence Berkeley National Lab. 
+His research interests lie in developing new computational imaging modalities to observe the structure and function of materials at high resolution and sensitivity.
+He is one of the core developers of the phase-retrieval modules in the [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source code.
+He is the technology editor for `Elemental Microscopy`, with extensive experience in using web-based open-source tools for pedagogy and science-communication.
+[Email](mailto:gvarnavides@berkeley.edu)
+[Website](https://gvarnavides.com/)
 
-## Editorial Board
 
-`Beth Dickey` is the Department Head and Teddy and Wilton Hawkins Distinguished Professor of the [Materials Science and Engineering](https://www.mse.engineering.cmu.edu/index.html) department at [Carnegie Mellon](https://www.cmu.edu/). She is a Fellow of the Microscopy Society of America and of the American Ceramic Society, and is a member of the World Academy of Ceramics. (ecdickey@cmu.edu)
 
-`Georgios Varnavides` is a Miller Fellow postdoc working at the University of California, Berkeley and Lawrence Berkeley National Lab. (gvarnavides@berkeley.edu )
 
+```{important}
+We are currently recruiting additional editoris and members of the editorial board! 
+Contact [Colin](mailto:cophus@stanford.edu) if you are interested.
+```
+
+
+## Editorial Board
 
 
-We are currently recruiting additional members of the editorial board! Contact [Colin Ophus](mailto:cophus@gmail.com) if you are interested.
+`Beth Dickey` is the Department Head and Teddy and Wilton Hawkins Distinguished Professor of the [Materials Science and Engineering](https://www.mse.engineering.cmu.edu/index.html) department at [Carnegie Mellon](https://www.cmu.edu/). 
+She is a Fellow of the Microscopy Society of America and of the American Ceramic Society, and is a member of the World Academy of Ceramics.
+[Email](mailto:ecdickey@cmu.edu)
 
 ---
 
 ## Technology
 
 The Elemental Microscopy journal was developed by the [Curvenote](https://curvenote.com/mission) team and built with open source [MyST Markdown](https://mystmd.org) components.
 
-`Rowan Cockett` is the CEO and co-founder of [Curvenote](https://curvenote.com), which is an interactive, online writing and publishing platform for science, with dedicated integrations to Jupyter. Rowan is a core developer of [MyST Markdown](https://mystmd.org/) and has a Ph.D. in computational geophysics from the University of British Columbia (UBC) where he worked on large-scale simulation and parameter estimation package for geophysical processes (electromagnetics, fluid-flow, gravity, etc.).
+`Rowan Cockett` is the CEO and co-founder of [Curvenote](https://curvenote.com), which is an interactive, online writing and publishing platform for science, with dedicated integrations to Jupyter. 
+Rowan is a core developer of [MyST Markdown](https://mystmd.org/) and has a Ph.D. in computational geophysics from the University of British Columbia (UBC) where he worked on large-scale simulation and parameter estimation package for geophysical processes (electromagnetics, fluid-flow, gravity, etc.).
 
-The larger [Curvenote team](https://curvenote.com/mission) including `Steve Purves`, `Franklin Koch` and `Mike Morrison` have been in involved in the design and development of Elemental Microscopy.
+The larger [Curvenote team](https://curvenote.com/mission) including `Steve Purves`, `Franklin Koch`, and `Mike Morrison` have been in involved in the design and development of Elemental Microscopy.
 
 ---
 

index.md

@@ -3,6 +3,10 @@ title: Elemental Microscopy
 description: Elemental Microscopy is an online journal published by the Microscopy Society of America. Our articles are highly interactive, leveraging the power of open-source scientific programming communities, and modern internet technologies.
 ---
 
-`Elemental Microscopy` is an online journal published by the [Microscopy Society of America](https://www.microscopy.org/). Our articles are highly interactive, leveraging the power of open-source scientific programming communities, and modern internet technologies.
+`Elemental Microscopy` is an online journal published by the [Microscopy Society of America](https://www.microscopy.org/).
+Our articles are highly interactive, leveraging the power of open-source scientific programming communities, and modern internet technologies.
 
-We will offer review and tutorial treatments of key topics, ranging from fundamental theory, instrumentation advancements, experimental methods and data analysis. These articles offer cutting-edge insights into emerging applications in a variety of areas including **biology**, **life sciences**, **geology**, **engineering**, **materials science**, **nanoscience**, **physics** and **archeology**. With embedded video, interactive code and data content, the publication serve as excellent educational resources for the microscopy and the broader science community. Regularly updated and developed specifically for a digital environment, this journal is a dynamic and enduring reference resource for students, researchers, and practitioners in microscopy.
+We offer reviews and tutorial treatments of key topics in **microscopy**, ranging from fundamental theory, instrumentation advancements, experimental methods and data analysis. 
+These articles offer cutting-edge insights into emerging applications in a variety of areas including **biology**, **life sciences**, **geology**, **engineering**, **materials science**, **nanoscience**, **physics**, and **archeology**. 
+With embedded video, interactive code, and data content, the publications serve as excellent educational resources for the microscopy and the broader science community. 
+Regularly updated and developed specifically for a digital environment, this journal is a dynamic and enduring reference resource for students, researchers, and practitioners in microscopy.

myst.yml

@@ -3,13 +3,25 @@ project:
   title: Elemental Microscopy
   open_access: true
   abbreviations:
+    APC: article processing charge
     CC BY 4.0: Creative Commons Attribution 4.0 International
     DOE: Department of Energy
+    DOI: digital object identifier
     MyST: Markedly Structured Text
     NCEM: National Center for Electron Microscopy
     TEM: transmission electron microscopy
     STEM: scanning transmission electron microscopy
+    S/TEM: scanning transmission electron microscopy
+    MSA: microscopy society of America
     US: United States
+  toc:
+    # Auto-generated by `myst init --write-toc`
+    - file: index.md
+    - file: overview.md
+    - file: articles.md
+    - file: writing-an-article.md
+    - file: editors.md
+
 site:
   title: Elemental Microscopy
   logo_text: EM

overview.md

@@ -3,33 +3,87 @@ title: Overview
 description: Publishing in Elemental Microscopy allows you to publish experimental data using highly interactive figures.
 ---
 
-Interactivity
-: One major benefit of publishing in `Elemental Microscopy` is that you can publish experimental data using **highly interactive figures**. These include:
 
-- **Images** where you can zoom in, change the contrast levels, flip between channels such as raw and processed, modify colormaps, and overlay additional information.
+## Overview
 
-- **Movies** embedded directly in the text with the ability to play back at any speed, show live analysis, and all of the other interactive options available for images.
+Publishing in `Elemental Microscopy` (`EM`) provides a groundbreaking way to share experimental data through **highly interactive figures** and **dynamic content**. 
+EM is built for researchers who want to go beyond static PDFs, offering tools to publish open-access articles that integrate data, code, and multimedia while promoting transparency, reproducibility, and innovative publishing tools.
 
-- **Plotting Data** which can be expanded to show statistics, sources of input data and error bars, and correlation between channels.
+Publication in `EM` is currently **free**, though we will be introducting an APC in  2026. 
 
-- **3D Volumes** with control over the viewing direction and magnification, isosurface levels, slice positions, and embedded measurements.
+---
+
+## Interactivity
+
+One of the most significant advantages of publishing in `Elemental Microscopy` is the ability to include **interactive figures**:
+
+- **Images**: Readers can zoom in, adjust contrast, flip between raw and processed data channels, overlay information, and customize colormaps.  
+- **Movies**: Embed movies directly within your manuscript, enabling readers to adjust playback speed, view live analyses, or interact with annotations in real time.  
+- **Plotting data**: Add plots that allow readers to expand visualizations, explore statistics, view error bars, and compare data across multiple channels interactively.  
+- **3D volumes**: Incorporate volumetric data with tools to control viewing angles, magnifications, slice positions, and isosurface levels, making complex datasets more accessible.  
+- **Anything else you can imagine**: You can include any python or jupyter tools you have developed for your research directly in your articles.
+
+Interactivity can make your research more engaging and enable readers to explore your science in unprecedented depth.
+
+---
+
+## Code
+
+`Elemental Microscopy` is built on the [**Jupyter Book**](https://jupyterbook.org/en/stable/intro.html) publishing platform and [**MyST Markdown**](https://mystmd.org/) typesetting language, allowing seamless integration of [**Jupyter notebooks**](https://jupyter.org/). 
+Authors can:
+
+- Reproduce workflows for visualization, analysis, and simulation directly in the article.  
+- Save time by publishing pre-existing Jupyter notebooks without needing to reformat them into LaTeX or Word.  
+- Embed executable code snippets that readers can run, fostering deeper engagement with your work.  
+
+This approach eliminates tedious reformatting and promotes transparent, reproducible research.
 
 ---
 
-Code
-: Built on the Jupyter Book publishing platform and MyST markdown language, `Elemental Microscopy` articles can include Jupyter notebooks which reproduce visualization, analysis, and simulation workflows. Authors can save time by publishing notebooks directly rather than rewriting into LaTeX or Word formats, and then typesetting into journal-specific formats.
+## Flexibility
+
+With **flexible article lengths**, EM supports diverse contributions:
+
+- Detailed tutorials and reviews.  
+- In-depth explorations of methodologies.  
+- Compact studies focusing on specific microscopy techniques.  
+
+Authors have the freedom to adapt the scope of their articles to meet the needs of the microscopy community.
 
 ---
 
-Flexibility
-: With lengths of approximately 5,000–30,000 words, `Elemental Microscopy` offer an opportunity to develop a theme in greater detail than is possible in a traditional journal article, yet more concisely than would be expected in a full-length book.
+## Preprints and Peer Review
+
+`Elemental Microscopy` supports an **open preprint and peer review model**:
+
+- **Preprints**: Publish a draft version of your article with a "preprint" label to solicit community feedback.  
+- **Peer Review**: Articles undergo an open peer review process.
+Reviewer comments are published alongside the article, ensuring transparency and accountability.
+Reviewers can choose to remain anonymous or disclose their identities.
+
+Accepted articles have the "preprint" label removed, with all referee reports permanently attached, offering a clear record of the review process.
 
 ---
 
-Preprints and Peer Review
-: You can publish the initial version of a scientific paper on the `Elemental Microscopy` platform, marked as a preprint version. EM articles will then go through a peer review process. After passing this review, accepted articles will have the preprint label removed and have all referee reports attached to the paper. Reviewers may opt to publish their names alongside their review, or remain anonymous.
+## Open Access
+
+All articles in EM are published under the **CC BY 4.0 license**, ensuring:
+
+- **Open Access**: Articles are freely available for anyone to read, share, and reuse.  
+- **Transparency**: Inline links to raw data, code repositories, and supporting materials make your research fully reproducible.  
+- **Author Rights**: Authors retain copyright over their work.  
+
+This model aligns with the principles of open science and maximizes the impact of your research.
 
 ---
 
-Open Access
-: All `Elemental Microscopy` articles will be published under a CC BY 4.0 open access license. Each article will contain not only the code required to produce all results and figures, but also inline links to raw data and source code repositories.
+## How to Get Started
+
+Ready to submit your article or want to learn more?
+Visit [elementalmicroscopy.com](https://www.elementalmicroscopy.com) or contact the editorial team:
+
+- [Colin Ophus](mailto:cophus@stanford.edu), Founding Editor-in-Chief  
+- [Georgios Varnavides](mailto:gvarnavides@berkeley.edu), Technology Editor  
+
+We look forward to helping you publish cutting-edge, interactive microscopy research with EM!
+